PROCHECK-NMR. PROCHECK v.3.4 - Parameter file (procheck_nmr.prm) ---------------------------- Note: Listing options and colour definitions are given at the end of the file. Colour all plots? ----------------- Y <- Produce all plots in colour (Y/N)? Which plots to produce ---------------------- a. Geometry plots -------------- Y <- 1. Ramachandran plot (Y/N)? Y <- 2. Gly & Pro Ramachandran plots (Y/N)? Y <- 3. Chi1-Chi2 plots (Y/N)? N <- 4. Residue Phi torsion angle plots (Y/N)? N <- 5. Residue Psi torsion angle plots (Y/N)? Y <- 6. Residue Chi-1 plots (Y/N)? Y <- 7. Residue Chi-2 plots (Y/N)? Y <- 8. Residue Ramachandran plots (Y/N)? N <- 9. Residue chi1-chi2 plots (Y/N)? Y <- 10. Ensemble geometry (Y/N)? Y <- 11. Equivalent resolution (Y/N)? Y <- 12. Model-by-model secondary structures (Y/N)? b. Restraint analyses ------------------ Y <- 13. Distance restraints plot (Y/N)? Y <- 14. Restraint differences plot (Y/N)? Y <- 15. Numbers of distance restraints (Y/N)? Y <- 16. Actual distance - restraint summary (Y/N)? Y <- 17. Violation frequency summary (Y/N)? Y <- 18. Restraint statistics (Y/N)? N <- 19. Restraint spans (Y/N)? Y <- 20. Residue-by-residue restraint violations (Y/N)? Y <- 21. Model-by-model violations (Y/N)? +-----------------+ | PLOT PARAMETERS | +-----------------+ a. G E O M E T R Y P L O T S 1. Ramachandran plot -------------------- N <- Separate page for each model in the ensemble (Y/N)? Y <- Shade in the different regions (Y/N)? Y <- Print the letter-codes identifying the different regions (Y/N)? Y <- Draw line-borders around the regions (Y/N)? N <- Show only the core region (Y/N)? 1 <- Label residues in: 0=disallow,1=generous,2=allow,3=core regions 1.0 <- Size of data-points (0.0-2.0) N <- Plot filled-in data points (Y/N)? Y <- Show model numbers inside data points (Y/N)? N <- Produce a COLOUR PostScript file (Y/N)? WHITE <- Background colour WHITE <- Region 0: Disallowed CREAM <- Region 1: Generous YELLOW <- Region 2: Allowed RED <- Region 3: Most favourable, core, region BLACK <- Colour of markers in favourable regions RED <- Colour of markers in unfavourable regions N <- Produce "publication version" of Ramachandran plot (Y/N)? 2. Gly & Pro Ramachandran plots ------------------------------- -3.0 <- Cut-off value for labelling of residues Y <- Plot all 20 Ramachandran plots (Y/N)? N <- Produce a COLOUR PostScript file (Y/N)? WHITE <- Background colour CREAM <- Lightest shaded regions on plots GREEN <- Darkest shaded regions on plots YELLOW <- Colour of markers in favourable regions RED <- Colour of markers in unfavourable regions 3. Chi1-Chi2 plots ------------------ -3.0 <- Cut-off value for labelling of residues N <- Produce a COLOUR PostScript file (Y/N)? WHITE <- Background colour CREAM <- Lightest shaded regions on plots GREEN <- Darkest shaded regions on plots YELLOW <- Colour of markers in favourable regions RED <- Colour of markers in unfavourable regions 4-9. Dihedral angle frequency distributions ------------------------------------------- Y <- Plot histograms, rather than show successive values (Y/N)? 0.0 <- Circ. var. cut-off (residues with lower values not plotted) Y <- Background shading (Y/N)? N <- Produce a COLOUR PostScript file (Y/N)? WHITE <- Background colour of page CREAM <- Background colour on graphs PURPLE <- Shading of region representing dihedral angle restraints YELLOW <- Colour for favourable G-factor scores RED <- Colour for unfavourable G-factor scores YELLOW <- Colour for accessibility & circular variance dials N <- Omit circular variance value and dial (Y/N)? N <- Omit G-factor value and shaded square (Y/N)? N <- Omit accessibility symbol (Y/N)? N <- Splay model-numbering on the 2D plots (Y/N)? 10. Ensemble geometry --------------------- 1 2 < Which 2 main graphs to be printed (see Note 2 for full list) Y <- Background shading on main graphs (Y/N)? 2.0 <- Number of standard deviations for highlighting Y <- Show shading representing estimated accessibility (Y/N)? N <- Produce a COLOUR PostScript file (Y/N)? WHITE <- Background colour CREAM <- Background shading on main graphs PURPLE <- Colour of histogram bars on main graphs RED <- Colour of highlighted histogram bars BLUE <- Minimum accessibility colour (buried regions) WHITE <- Maximum accessibility colour YELLOW <- Colour for favourable G-factor scores RED <- Colour for unfavourable G-factor scores YELLOW <- Colour for schematic of the secondary structure YELLOW <- Colour for accessibility & circular variance dials Note 2 ------ The 2 main graphs on the Ensemble Residue properties plot can be any 2 from the following list of options:- 1. Absolute deviation from mean Chi-1 value (excl. Pro) 2. Absolute deviation from mean of omega torsion 3. C-alpha chirality: abs. deviation of zeta torsion 11. Equivalent resolution ------------------------- Y <- Background shading (Y/N)? N <- Produce a COLOUR PostScript file (Y/N)? WHITE <- Background colour CREAM <- Background shading on each graph PURPLE <- Colour of band 12. Model-by-model secondary structures --------------------------------------- Y <- Show shading representing estimated accessibility (Y/N)? N <- Produce a COLOUR PostScript file (Y/N)? WHITE <- Background colour BLUE <- Minimum accessibility colour (buried regions) WHITE <- Maximum accessibility colour YELLOW <- Colour for schematic of the secondary structure b. R E S T R A I N T A N A L Y S E S General parameters ------------------ N <- Define short/medium/long-range restraints by dist - see Note (Y/N)? 0.0 3.5 <- Upper and lower distance defining short-range restraints 3.5 5.0 <- " " " " " medium-range " 5.0 10.0 <- " " " " " long-range " YELLOW <- Colour for long-range restraints LIME GREEN <- Colour for medium-range restraints CYAN <- Colour for short-range restraints Note ---- If the above parameter is set to Y, the restraints will be classed as short, medium or long-range according to the distance ranges defined above. If the parameter is set to N, the default definition will be taken where the ranges depend on the sequence separation of the residues involved in each restraint, as follows:- Short-range - restraint is between atoms of same residue Medium-range - restraint links residues whose sequence separation is between i + 1 and i + 4 Long-range - restraint links residues whose sequence separation is greater than 4 residues 13-14. Distance restraints and Restrain differences plots --------------------------------------------------------- Y <- Include all short-range restraints (as defined above) (Y/N)? Y <- " " medium-range " " " " (Y/N)? Y <- " " long-range " " " " (Y/N)? Y <- Include NOE distance restraints (Y/N)? Y <- Include H-bond distance restraints (Y/N)? Y <- Include disulphide distance restraints (Y/N)? Y <- Show only violated restraints (Y/N)? Y <- Exclude duplicate restraints within the same residue (Y/N)? Y <- Background shading on main graphs (Y/N)? N <- Produce a COLOUR PostScript file (Y/N)? WHITE <- Background colour CREAM <- Background shading on main graphs PINK <- Shading for regions outside upper restraint bounds ORANGE <- Shading for regions outside lower restraint bounds 15-17. Summaries of distance restraints and differences ------------------------------------------------------- Y <- Separate page for each graph (Y/N)? Y <- Background shading on main graphs (Y/N)? N <- Produce a COLOUR PostScript file (Y/N)? WHITE <- Background colour CREAM <- Background shading on main graphs PURPLE <- Colour for upper-bound restraints SKY BLUE <- Colour for lower-bound restraints RED <- Colour for upper-bound restraint violations PINK <- Colour for lower-bound restraint violations 18. Restraint statistics ------------------------ N <- Produce a COLOUR PostScript file (Y/N)? WHITE <- Background colour PURPLE <- Colour for upper-bound restraints SKY BLUE <- Colour for lower-bound restraints RED <- Colour for upper-bound restraint violations PINK <- Colour for lower-bound restraint violations 19-21. Restraint spans, residue-by-residue and model-by-model violations ------------------------------------------------------------------------ Y <- Include all short-range restraints (as defined above) (Y/N)? Y <- " " medium-range " " " " (Y/N)? Y <- " " long-range " " " " (Y/N)? Y <- Include NOE distance restraints (Y/N)? Y <- Include H-bond distance restraints (Y/N)? Y <- Include disulphide distance restraints (Y/N)? Y <- Background shading on main graphs (Y/N)? Y <- Show shading representing estimated accessibility (Y/N)? N <- Produce a COLOUR PostScript file (Y/N)? WHITE <- Background colour CREAM <- Background shading on main graphs BLUE <- Minimum accessibility colour (buried regions) WHITE <- Maximum accessibility colour SKY BLUE <- Colour for favourable G-factor scores RED <- Colour for unfavourable G-factor scores YELLOW <- Colour for schematic of the secondary structure YELLOW <- Colour for accessibility dials CYAN <- Colour for histograms of restraints per residue RED <- Colour for restraint violations Colours (up to 50 can be defined) ------- 0.0000 0.0000 0.0000 'BLACK' <- Colour 1 1.0000 1.0000 1.0000 'WHITE' <- Colour 2 1.0000 0.0000 0.0000 'RED' <- Colour 3 0.0000 1.0000 0.0000 'GREEN' <- Colour 4 0.0000 0.0000 1.0000 'BLUE' <- Colour 5 1.0000 1.0000 0.0000 'YELLOW' <- Colour 6 1.0000 0.7000 0.0000 'ORANGE' <- Colour 7 0.5000 1.0000 0.0000 'LIME GREEN' <- Colour 8 0.5000 0.0000 1.0000 'PURPLE' <- Colour 9 0.5000 1.0000 1.0000 'CYAN' <- Colour 10 1.0000 0.5000 1.0000 'PINK' <- Colour 11 0.3000 0.8000 1.0000 'SKY BLUE' <- Colour 12 1.0000 1.0000 0.7000 'CREAM' <- Colour 13 0.0000 1.0000 1.0000 'TURQUOISE' <- Colour 14 1.0000 0.0000 1.0000 'LILAC' <- Colour 15 0.8000 0.0000 0.0000 'BRICK RED' <- Colour 16 0.5000 0.0000 0.0000 'BROWN' <- Colour 17 0.9700 0.9700 0.9700 'LIGHT GREY' <- Colour 18 0.9000 0.9000 0.9000 'MID GREY' <- Colour 19 0.8000 0.0000 1.0000 'MAUVE' <- Colour 20 -------------------------------------------------------------------------- File-handles ------------ N <- Add 9-character description of plot to each plot filename (Y/N)? (eg p1nmr_01_ramachand.ps, rather than p1nmr_01.ps) Y <- Print name of plotfile in bottom-left corner of plot (Y/N)? Y <- Combine all pages of same plot into single PostScript file (Y/N)? --------------------------------------------------------------------------